diagonal matrix to square matrix Post: 302352541

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Top Forums Shell Programming and Scripting diagonal matrix to square matrix Post 302352541 by durden_tyler on Friday 11th of September 2009 06:22:45 PM

09-11-2009

Registered User

Here's a Perl solution for the type of data you posted:

Code:

$
$ cat diagmtx.txt
"244901_AT" 1.000 0.234 0.435 0.123 0.012 0.102 0.325 0.412 0.087 0.098
"243903_AT" 1.000 0.111 0.412 0.115 0.058 0.091 0.190 0.045 0.058
"244501_AT" 1.000 0.205 0.542 0.335 0.054 0.117 0.203 0.125
"254902_AT" 1.000 0.587 0.159 0.357 0.258 0.654 0.341
"247906_AT" 1.000 0.269 0.369 0.687 0.145 0.125
"242901_AT" 1.000 0.222 0.451 0.134 0.333
"243906_AT" 1.000 0.112 0.217 0.095
"244908_AT" 1.000 0.508 0.701
"294902_AT" 1.000 0.663
"245902_AT" 1.000
$
$ # show the Perl program
$ cat convert_2.pl
#!/usr/bin/perl -w
@mtx = ();
$file = $ARGV[0];
open (F,$file) or die "Can't open $file: $!";
while(<F>){
  @x = split;
  $id = shift @x;
  $therest = "@x\n";
  shift @x;
  push @mtx, [@x];
  if ($.==1) {
   print;
  } else {
    print $id," ";
    for($i=0;$i<=$.-2;$i++) {
      print $mtx[$i][0]," ";
      shift @{$mtx[$i]};
    }
    print $therest;
  }
}
close (F) or die "Can't close $file: $!";
$
$ perl convert_2.pl diagmtx.txt
"244901_AT" 1.000 0.234 0.435 0.123 0.012 0.102 0.325 0.412 0.087 0.098
"243903_AT" 0.234 1.000 0.111 0.412 0.115 0.058 0.091 0.190 0.045 0.058
"244501_AT" 0.435 0.111 1.000 0.205 0.542 0.335 0.054 0.117 0.203 0.125
"254902_AT" 0.123 0.412 0.205 1.000 0.587 0.159 0.357 0.258 0.654 0.341
"247906_AT" 0.012 0.115 0.542 0.587 1.000 0.269 0.369 0.687 0.145 0.125
"242901_AT" 0.102 0.058 0.335 0.159 0.269 1.000 0.222 0.451 0.134 0.333
"243906_AT" 0.325 0.091 0.054 0.357 0.369 0.222 1.000 0.112 0.217 0.095
"244908_AT" 0.412 0.190 0.117 0.258 0.687 0.451 0.112 1.000 0.508 0.701
"294902_AT" 0.087 0.045 0.203 0.654 0.145 0.134 0.217 0.508 1.000 0.663
"245902_AT" 0.098 0.058 0.125 0.341 0.125 0.333 0.095 0.701 0.663 1.000
$
$

I think summer_cherry's program is a much more optimized version. It -
(i) does not store the entire N X N square matrix in any data structure.
(ii) stores only the information present in the file, since that is sufficient to generate the other half of the square matrix.
(iii) uses hashes for fast access.

My second version uses a multi-dimensional array to store only the necessary information i.e. everything after the "id" and "1.000" per element. It also keeps on chopping the array element right after it is printed, by using the "shift" operator. So while the run time would be higher for this, the memory consumption should be lesser.

HTH,
tyler_durden

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clanht

clanht.f(3)							      LAPACK							       clanht.f(3)

NAME

       clanht.f -

SYNOPSIS

   Functions/Subroutines
       REAL function clanht (NORM, N, D, E)
	   CLANHT returns the value of the 1-norm, or the Frobenius norm, or the infinity norm, or the element of largest absolute value of a
	   complex Hermitian tridiagonal matrix.

Function/Subroutine Documentation
   REAL function clanht (characterNORM, integerN, real, dimension( * )D, complex, dimension( * )E)
       CLANHT returns the value of the 1-norm, or the Frobenius norm, or the infinity norm, or the element of largest absolute value of a complex
       Hermitian tridiagonal matrix.

       Purpose:

	    CLANHT  returns the value of the one norm,	or the Frobenius norm, or
	    the  infinity norm,  or the  element of  largest absolute value  of a
	    complex Hermitian tridiagonal matrix A.

       Returns:
	   CLANHT

	       CLANHT = ( max(abs(A(i,j))), NORM = 'M' or 'm'
			(
			( norm1(A),	    NORM = '1', 'O' or 'o'
			(
			( normI(A),	    NORM = 'I' or 'i'
			(
			( normF(A),	    NORM = 'F', 'f', 'E' or 'e'

	    where  norm1  denotes the  one norm of a matrix (maximum column sum),
	    normI  denotes the	infinity norm  of a matrix  (maximum row sum) and
	    normF  denotes the	Frobenius norm of a matrix (square root of sum of
	    squares).  Note that  max(abs(A(i,j)))  is not a consistent matrix norm.

       Parameters:
	   NORM

		     NORM is CHARACTER*1
		     Specifies the value to be returned in CLANHT as described
		     above.

	   N

		     N is INTEGER
		     The order of the matrix A.  N >= 0.  When N = 0, CLANHT is
		     set to zero.

	   D

		     D is REAL array, dimension (N)
		     The diagonal elements of A.

	   E

		     E is COMPLEX array, dimension (N-1)
		     The (n-1) sub-diagonal or super-diagonal elements of A.

       Author:
	   Univ. of Tennessee

	   Univ. of California Berkeley

	   Univ. of Colorado Denver

	   NAG Ltd.

       Date:
	   September 2012

       Definition at line 102 of file clanht.f.

Author
       Generated automatically by Doxygen for LAPACK from the source code.

Version 3.4.2							  Tue Sep 25 2012						       clanht.f(3)